On May 5, 2018, ASA published the first full set of new Genomically-Enhanced EPDs (GE-EPDs) generated through the IGS Multi-breed Genetic Evaluation powered by BOLT. Now it has been more than a year since the first release, and ASA publishes GE-EPDs every week. That is a tremendous success for ASA and its members to have access to more accurate GE-EPDs calculated by the most advanced statistical model and software in the world. While the IGS science team continues to make improvements in accuracies of GE-EPDs, the question that may come is what’s the next application of genomics in beef cattle? How can genomics help the beef industry besides calculating GE-EPDs? Below are some of my thoughts:
New marker subsets
It is very important to remove DNA markers with inconsistent effects or no effects in different breeds from being used in multi-breed genomic predictions (similar to IGS). Based on a research study that I performed at Iowa State University (ISU), I selected a subset of around 2,300 markers from approximately 50,000 markers that are highly associated with economically-relevant traits in beef cattle with consistent effects across different breeds (known as Mahdi Saatchi Reduced Panel or MSRP). This marker subset has been used in the IGS Multi-breed Genetic Evaluation powered by BOLT since its first release in 2018. We continue to identify new markers within our populations of beef breeds that have greater significance and effect on production and other economically-relevant traits. The new marker subsets will be developed and used to improve the accuracy of our genomic predictions.
There are many other traits that are important for the beef industry, but we don’t have EPDs or GE-EPDs for them at this time because they are hard or expensive to measure. But genomics can help identify genetic markers associated with those traits in a small recorded population and then be used for selection in a larger population. For example, Bovine Respiratory Disease (BRD) is the leading cause of illness and death for the backgrounding and feedlot cattle industries. Evidence that BRD susceptibility has a genetic component is demonstrated by many research studies. How about having GE-EPDs for BRD susceptibility where we can select our beef cattle to be more resistant/resilient to BRD?
Another example is beef healthfulness. One of the research studies that I was involved with during my postdoc at ISU looked at the genetic basis of fatty acid composition in beef cattle. We identified some genetic markers that impact fatty acid composition, which can be used to select for improved beef healthfulness. That means beef cattle breeders can have some genomic tools in the future to select for healthier beef (lower cholesterol and higher healthy fatty acids such as omega-3). How could that technology change the beef industry?
Inbreeding does not create undesirable recessive genes, but it could lead to a decline in average phenotypic performance especially for reproductive traits, known as inbreeding depression. On the other hand, heterosis (hybrid vigor), which is the opposite of inbreeding depression, is the advantage gained from outbreeding by crossing different lines or breeds. Genomics is a great tool to measure the levels of inbreeding or outbreeding more accurately. If we can characterize the effects of inbreeding depression and heterosis across the genome (which genetic markers can cause inbreeding depression or heterosis) then we should be able to optimize our breeding decisions to benefit more from heterosis and suffer less from inbreeding depression. Does this sound like a cool tool to you?
Mutations (changing DNA codes from one form to another) are the basis of evolution and create the variations among different species, breeds, and individuals within a breed. Some mutations can cause the gene to lose its functionality (broken gene). If the gene is vital for survival, then an individual with two copies of a broken gene can die early in life (embryonic lethality). Most of the broken genes are still unknown in livestock populations, but we can use a group of genetic markers together to tag some of those lethal genes in the genome (known as lethal haplotype). Several of those lethal haplotypes have been identified in dairy cattle, and now dairy breeders have a genomic tool to manage and control them. I have no doubt that there are harmful lethal haplotypes segregating in our beef populations. Do you also think that we can improve our cows’ fertility by detecting and managing some of those lethal haplotypes in our beef cattle?
Estimation of breed composition of an animal is an important piece of estimating EPDs in any multi-breed genetic evaluation. We will keep track of an animal’s pedigree up to the founders to determine its breed composition percentages. However, genomics can provide a more accurate estimation of breed composition for a genotyped animal by looking at what percentage of genes he or she inherited from each ancestor breed. That means a SimAngus™ bull currently with a 5/8 SM 3/8 AN breed composition estimate could actually have inherited more or less than 5/8 Simmental genes from his ancestors! If genomics could help us improve the accuracy of GE-EPD, why couldn’t it help us to improve the accuracy of breed composition estimation?
These are just a few examples where genomics can help our industry in the future. I hope to see some of these applications of genomics in the beef industry during my career.